Blender - Plot viewport-independent 2D-Labels
The features in blender for this task are not so advanced, so I would suggest one of two options...


Load in Empty objects and name them usefully, enabling the objects display -> name option in the object buttons. 
(note, these names wont render)
Create 3d text objects for each name (reduce the curve resolution to ~4 or so, for faster display), these will render which is their main advantage.
(note, wont point towards the view though you could constrain them to face the camera).


You say that the amount of object would be huge and hard to view in the outliner. To workaround this you could...


Give them a parent, the outliner will nest them under the parent.
Put them on a second layer (probably a good idea anyway), then set the outliner to only view visible layers.


Other alternatives exist like using Python to draw text in the view-port or converting curve data to grease-pencil. But Im not sure these are worth the extra hassle of simply creating named empties or text objects.